Hi All,
Which default atlas does FreeSurfer 5.3 use for the segmentation of subcortical
structures?
Thanks
Theo
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The informat
I just tried to run my first recon-all.
What now?
[Logo]
Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP.
Laboratory for Brain & Heart Health
School of Kinesiology
Western University
Room 402, Arthur & Sonia Labatt Health Sciences Building
London, ON, Canada, N6A 5B9
Tel: (519) 661-2111 x 89066
Hi Brad
it looks like the recon failed as you ran out of disk space:
cvarput: ncid 5: No space left on device
miicv_put: MINC package entry point
nu_evaluate: crashed while running mincmath (termination status=768)
nu_correct: crashed while running nu_evaluate (termination status=768)
as for w
Hi all,
I am using FS with data from 2 different studies that were acquired on the
same MRI-machine with the same T1 and FLAIR sequences. Unfortunately, the
group sizes are not very balanced, with 31 controls, 16 obese and 32
diabetes patients.
Is the GLM for thickness used in FS very sensitive t
Hi Eelco
it isn't really a question of whether our implementation is senstitive to
this. It's that in general your power will be constrained by the size of
the smaller group (I assume this is Type 2 diabetes by the way).
cheers
Bruce
On Thu, 13 Oct 2016, Eelco van Duinkerken wrote:
> Hi all,
Hi Eelco
it depends on how you setup your GLM. Are you trying to regress out the
effects of obesity in some way? If you give us more details I expect
someone else can answer your question (Doug!)
cheers
Bruce
On Thu, 13 Oct 2016, Eelco van Duinkerken
wrote:
Thanks for the quick reply!
S
Thanks for the quick reply!
So if I understand correctly, the power of say the controls vs. diabetes
(indeed it is type 2 diabetes) comparison is constrained by the sample size
of the obese group?
2016-10-13 11:02 GMT-03:00 Bruce Fischl :
> Hi Eelco
>
> it isn't really a question of whether our
Ah sorry for the low level of info. I am aiming to do a simple group
comparison, where I'm comparing thickness between controls and obese or
T2DM patients, regressing out the effect of age, sex and, hypertension. So
I created one thickness file with fwhm 10 containing all participants of
the 3 grou
According to this website
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferVersion3, Freesurfer v
3.0 uses Aseg atlas for the segmentation of subcortical structures.
It does not explicitly mention anything about Freesurfer v5.3 though.
On Thu, Oct 13, 2016 at 8:02 AM, AKUDJEDU, THEOPHILUS <
t.a
Thank you, Bruce for the rapid reply. I am running Freesurfer on a (Windows 10
based), virtual machine. I installed / set it up according to the directions
posted here:
https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVirtualImage
...specifically referring to the recommended me
you can always look in the recon-all script - the atlas (*.gca) file we
use is listed in there.
cheers
Bruce
On Thu, 13 Oct 2016, GAJENDRA KATUWAL (RIT Student)
wrote:
According to this website
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferVersion3, Freesurfer v
3.0 uses Aseg atlas for
Hi Brad
how much disk space do you have free? It looks like not enough as the
message I posted typically means you have run out of space on the sdisk
cheers
Bruce
On
Thu, 13 Oct 2016, Brad Matushewski wrote:
Thank you, Bruce for the rapid reply. I am running Freesurfer on a (Windows 10
b
Dear Eelco
years ago i posed a similar question on the FS email list
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-November/021386.html
a part of the response is below
>>> The other question is how mri_glmfit estimates the variance. Because I have
>>> only one subject in the patie
I think its referring to the hard disk space in the virtual machine. You
probably ran out which is not surprising, as the amount of free space
provided with the disk image is fairly small. The fact the your host
machine has 305Gb of HD on the host machine is unknown to the virtual
machine.
Se
Under Storage: Controller: SATA
Virtual Size: 20Gb
Actual Size: 17.35 Gb
Is there a way to expand this or do I have to delete and reinstall the virtual
machine?
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.e
I would appear that the allotted hard drive space is fixed as a function of the
Freesurfer installation. There does not appear to be an option to expand
allotted space either at time of installation or after the fact.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[ma
Thank you Jurgen!
That helps a lot. Good to know that the results are not driven by any
difference in varience.
Thanks all,
Eelco
2016-10-13 12:00 GMT-03:00 Juergen Haenggi :
> Dear Eelco
>
> years ago i posed a similar question on the FS email list
>
> https://mail.nmr.mgh.harvard.edu/pipermai
I was afraid this was the case. Normally in this situation I would say
set up a shared folder between the host and the virtual machines. But
unfortunately there is a known bug in the the MNI tools shipped with
freesurfer which makes this an incompatible arrangement.
The disk space was assigned
Would a feasible approach be to set up a dual-boot on my PC so that I can boot
directly into either a Windows or Linux environment?
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Z K
Sent: Thursday, October 13
Yes, that would be a good option. Its a little work but here is a guide
that I dug up which helps explain the process. For the version of linux
to use... I would recommend Ubuntu 14.04.5 LTS
(https://www.ubuntu.com/download/alternative-downloads)
On 10/13/2016 01:25 PM, Brad Matushewski wrote
Dear expert
I'm beginner in using Freesurfer and I really need your help.
However I've read all related responded questions about paralleling process. I
found -openmp N flag to do that, but I don't understand its correct location in
'recon-all'. I used it as follows but it doesn't work. Also I w
You provided us with very little information to help you solve your
problem. Please read the "How to describe you problem" section of our wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
However, after looking at your exact command, it appears you are using
the "long dash" (or em
Dear All,
I am trying to get started with FreeSurfer. I would like to know if the Mac OS
versions (Yosemite, Sierra) are compatible and can run the FreeSurfer, if not
please let me know which is the latest Mac OS version that supports FreeSurfer.
I tried installing it on Mac OS Sierra but it
Doug-
Any further thoughts on this?
On 10/05/2016 04:47 PM, Joel Bruss wrote:
> Doug-
>
> I'm sooo close but something isn't right. I've run:
>
> 1)mri_vol2sur to sampel the ROI in subA surface space
>
> 2) mri_cor2label to convert it to a label
>
> 3) mri_label2lable to push it to subB
>
> 4)
Hello Doug and Freesurfers,We are having trouble unpacking DTI data collected in Bay7. Data are here: cd /autofs/eris/marco/tmp/seunThe error I get is this one, which prevents the nii file from being created:ERROR: mri_convertchild killed: segmentation violationIt looks like the problem doesn’t occ
25 matches
Mail list logo
